Principles of Enrichment, Isolation, Cultivation and Preservation of Prokaryotes
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Principles of Enrichment, Isolation, Cultivation and Preservation of Prokaryotes JÖRG OVERMANN
Introduction Currently, a total of 4700 validly published prokaryotic species are recognized (as of July 2002; DSMZ, 2002; Euzéby, 2001; Fig. 1). In contrast, the number of bacterial species present in just one type of forest soil has been estimated to be 13,000 or even 53,000 species (Torsvik et al., 1994; Sandaa et al., 1999). In light of these more recent findings, the earlier estimate of the fraction of already cultured bacterial species of 20% (Wayne et al., 1987) appears to be much too optimistic. This view is also supported by numerous molecular investigations of 16S rRNA gene sequences in natural bacterial assemblages that indicate a significant fraction of bacteria present in the environment has not yet been recovered by cultivation-based approaches (Fuhrman et al., 1992; Ward et al., 1992; Barns et al., 1994; DeLong et al., 1994; Hiorns et al., 1997; Kuske et al., 1997; Ludwig et al., 1997; Suzuki et al., 1997; Gich et al., 2001; Béjà et al., 2002). The 16S rRNA gene libraries of natural bacterial communities usually do not match sequences of strains isolated from the same or similar samples (Hiorns et al., 1997; Suzuki et al., 1997; Hugenholtz et al., 1998). Even a large cultivation campaign during which 659 bacterial isolates were obtained from grassland soil did not yield any strain with a 16S rRNA sequence corresponding to the dominant strains in the natural community (Felske et al., 1999). In some cases, this discrepancy may simply be the result of the low number of cultivation attempts, since even conventional cultivation trials continue to yield novel phylotypes of bacteria (Pinhassi et al., 1997; Suzuki et al., 1997) and the number of recognized species continuously increases at a rate of about 190 species per year (Fig. 1). In many instances, key reactions in biogeochemical cycles appear to be mediated not by the frequently isolated prokaryotes but rather by other prokaryotes that are phylogenetically unrelated and mostly not-yet-cultured. Examples include members of the Nitrosospira-group which (instead of Nitrosomonas spp.) catalyze nitrification in at least some environments
(Hastings et al., 1998; Schramm et al., 1999), Achromatium spp. and coccoid magnetotactic bacteria participating in the sulfur cycle (Spring et al., 1993), archaea which apparently mediate anaerobic methane consumption (Hinrichs et al., 1999), and novel type II methanotrophic bacteria oxidizing methane at atmospheric concentrations (Holmes et al., 1999; Roslev et al., 1999). Some environments harbor whole groups of entirely unknown bacteria and archaea, which most likely are important for the biogeochemical transformations (Hugenholtz et al., 1998). These include for instance members of the green filamentous bacteria (Coolen et al., 2002) or freshwater actinobacteria (Glöckner et al., 2000). In addition, first cultur
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